+Open data
-Basic information
Entry | Database: PDB / ID: 1bv4 | ||||||
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Title | APO-MANNOSE-BINDING PROTEIN-C | ||||||
Components | PROTEIN (MANNOSE-BINDING PROTEIN-C) | ||||||
Keywords | SUGAR BINDING PROTEIN / C-TYPE LECTIN / CALCIUM-BINDING PROTEIN / COLLECTIN | ||||||
Function / homology | Function and homology information Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / positive regulation of complement activation / galactose binding / negative regulation of viral process / positive regulation of protein processing / killing by host of symbiont cells ...Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / positive regulation of complement activation / galactose binding / negative regulation of viral process / positive regulation of protein processing / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / serine-type endopeptidase complex / phosphatidylinositol-4-phosphate binding / D-mannose binding / positive regulation of phagocytosis / antiviral innate immune response / complement activation, classical pathway / multivesicular body / calcium-dependent protein binding / protease binding / defense response to Gram-positive bacterium / innate immune response / signaling receptor binding / calcium ion binding / protein-containing complex / proteolysis / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Ng, K.K.-S. / Weis, W.I. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Ca2+-dependent structural changes in C-type mannose-binding proteins. Authors: Ng, K.K. / Park-Snyder, S. / Weis, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bv4.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bv4.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bv4_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 1bv4_full_validation.pdf.gz | 452.3 KB | Display | |
Data in XML | 1bv4_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 1bv4_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/1bv4 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/1bv4 | HTTPS FTP |
-Related structure data
Related structure data | 1buuC 1rdoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 13161.604 Da / Num. of mol.: 4 / Fragment: SUBTILISIN FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PINOMPAII / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JA221 / References: UniProt: P08661 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 36 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.2 Details: 12% PEG 8000, 100 MM NAMES, PH 6.1, 200 MM LICL, 2 MM EDTA 0.02%, NAN3, pH 6.2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1996 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 33667 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.2 / % possible all: 99.8 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RDO Resolution: 1.85→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.1 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.92 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3C / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.304 / % reflection Rfree: 10 % / Rfactor Rwork: 0.237 / Rfactor obs: 0.237 |